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comparison Paired_fastQ_trimmer.xml @ 0:548887c4227c draft

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author geert-vandeweyer
date Thu, 13 Feb 2014 08:21:01 -0500
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1 <tool id="Paired_fastQ_trimmer" name="Paired FastQ QC-Trimmer" >
2 <description></description>
3 <requirements>
4 <requirement type='package' version='1.92'>perl_module_threads</requirement>
5 <requirement type='package' version='1.46'>perl_module_threads_shared</requirement>
6 <requirement type='package' version='3.02'>perl_module_Thread_Queue</requirement>
7
8 </requirements>
9 <command interpreter="perl">Paired_fastQ_trimmer.pl -v 0 -i "$inputforward" -q "$trimq" -n "$readnames" -s "$style" -o $output1 -F $output3 -S $side -m $minlength
10 #if $IsPaired.paired=="true":
11 -I $inputreverse
12 -O $output2
13 #end if
14 </command>
15
16 <inputs>
17 <param name="trimq" value="30" type="integer" label="Quality Threshold (phred)" />
18 <param name="minlength" value="18" type="integer" label="Discard Reads shorter than this value as failed" />
19 <param name="readnames" value="@" type="text" label="First (eg 5) characters of the read names" />
20 <param name="style" type="select" label="Trimming Style to use" >
21 <option value='simple'>Simple 1bp-window trimming</option>
22 <option value='bwa'>BWA-Style trimming (bwa -q param)</option>
23 </param>
24 <param name="side" type="select" label="Which side of the reads should be trimmed" >
25 <option value='b'>Both 5' and 3'</option>
26 <option value='3'>3' only</option>
27 <option value='5'>5' only</option>
28 </param>
29 <conditional name="IsPaired">
30 <param name="paired" type="select" label="Is the data paired-end?">
31 <option value="false">Single-end</option>
32 <option value="true">Paired-end</option>
33 </param>
34 <when value='true'>
35 <param format="fastqsanger" name="inputforward" type="data" label="FASTQ file with Forward Reads" />
36 <param name='inputreverse' type='data' format='fastqsanger' label='FASTQ file with Reverse Reads' />
37 </when>
38 <when value='false'>
39 <param format="fastqsanger" name="inputforward" type="data" label="FASTQ to trim" />
40 </when>
41 </conditional>
42 </inputs>
43
44 <outputs>
45 <data format='fastqsanger' name="output1" label="${tool.name} on ${on_string}: Forward reads"/>
46 <data format='fastqsanger' name='output2' label="${tool.name} on ${on_string}: Reverse reads">
47 <filter>(IsPaired['paired'] == 'true')</filter>
48 </data>
49 <data format='fastqsanger' name='output3' label="${tool.name} on ${on_string}: Removed read pairs" />
50 </outputs>
51 <help>
52
53 **What it does**
54
55 This tool trims FASTQ files based on quality score. It handles paired-end data in a single step, supporting simple trimming and BWA-style trimming.
56
57
58 </help>
59 </tool>